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121,909 results • Page
47 of 2439
Sort: Rank
Rank
Views
Votes
Replies
3
votes
5
replies
2.0k
views
Flye Assembler Nano-Raw vs Nano-HQ options
Genome
assembly
nanopore
flye
9 months ago by
SomeOne
▴ 240
0
votes
1
reply
662
views
cell deconvolution tool Kassandra
cell
deconvolution
RNAseq
Kassandra
TPM
updated 9 months ago by
ATpoint
89k • written 9 months ago by
adR
▴ 130
0
votes
0
replies
472
views
News:
Course: Multivariate Data Analysis with R and vegan
R
vegan
Statistics
Multivariate-Data-Analysis
updated 9 months ago by
Ram
45k • written 9 months ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
1.5k
views
Low Salmon mapping rate even after stringent `fastp` (overrepresented GGGG permitted and troublesome Per tile sequence quality & Per base sequence co…
fastp
RNAseq
updated 9 months ago by
ATpoint
89k • written 9 months ago by
Quang
▴ 10
3
votes
3
replies
4.5k
views
News:
2nd Edition of the Biostar Handbook. New online course starts now.
biostar-handbook
updated 9 months ago by
anton.kochkov
• 0 • written 6.7 years ago by
Istvan Albert
103k
0
votes
1
reply
571
views
Clustering Challenges in Gene Expression Analysis Using WGCNA
r
updated 9 months ago by
andres.firrincieli
3.9k • written 9 months ago by
NDA
▴ 20
0
votes
2
replies
768
views
Holstein cow SNP reference haplotype panel with FORMAT and SAMPLES (genome ARS-UCD1.2)
cow
Holstein
SNP
reference-panel
9 months ago by
biology.may20
▴ 20
1
vote
2
replies
796
views
Plant diploid genome, phashed, CLR reads, PECAT
diploid
genome
Phased
9 months ago by
san96
▴ 190
0
votes
2
replies
1.5k
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
updated 9 months ago by
cpw
• 0 • written 16 months ago by
DGTool
▴ 290
0
votes
1
reply
488
views
Cluster id conversion into gene names
Cluster-4432.
Cluster-4432.3313
updated 9 months ago by
Mensur Dlakic
★ 30k • written 9 months ago by
Malik
• 0
1
vote
8
replies
2.0k
views
Tools for Subsampling Paired-End Reads to 25X Coverage ?
paired-end
fastq
depth
sequencing
coverage
updated 9 months ago by
Mensur Dlakic
★ 30k • written 9 months ago by
Sony
▴ 20
3
votes
3
replies
4.8k
views
6 follow
GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq
ATAC
Fragments
GeneActivity
RNA
Seurat
updated 9 months ago by
Mr
• 0 • written 3.3 years ago by
el24
▴ 50
4
votes
9
replies
3.8k
views
hd WGCNA - Preservation statistics (Zsummary & MedianRank)
hdWGCNA
WGCNA
updated 9 months ago by
andres.firrincieli
3.9k • written 2.8 years ago by
AKypR
▴ 10
0
votes
0
replies
392
views
No overlapping contigs problem
virus
haplotypecaller
gatk
updated 9 months ago by
GenoMax
153k • written 9 months ago by
Matheus
• 0
10
votes
13
replies
2.5k
views
undermined fastq and top unknown barcodes
bcl2fastq
updated 9 months ago by
GenoMax
153k • written 9 months ago by
1769mkc
★ 1.3k
2
votes
1
reply
709
views
Problem while replicating methylation predicting paper, looking for explanation
bioconductor
methylation
machine-learning
r
updated 9 months ago by
cmdcolin
★ 4.3k • written 9 months ago by
Junk
• 0
0
votes
0
replies
383
views
ssGSEA cross-species
ssGSEA
RNAseq
TPM
GSEA
9 months ago by
georgii.vdovin
• 0
4
votes
10
replies
1.6k
views
Batch correction of two RNA-Seq data sets
DESeq2
batch-correction
9 months ago by
gogeni5529
▴ 80
0
votes
0
replies
296
views
Plot meRIP bw data on single RNA
plot
meRIP
updated 9 months ago by
Ram
45k • written 9 months ago by
jia
• 0
1
vote
1
reply
903
views
Optimal Method for Chain File Generation: BLAT vs Minimap2 and MAF2Chain vs axtChain
Generation
paf2chain
axtChain
Tool
Chain
updated 9 months ago by
cmdcolin
★ 4.3k • written 9 months ago by
myoui3122010
▴ 30
2
votes
7
replies
2.1k
views
Which method should I use to merge scRNA-seq data, Cellranger aggr or Seurat?
scRNA-seq
CellRanger
hdWGCNA
Seurat
8 months ago by
Apprentice
▴ 190
0
votes
0
replies
348
views
Clonality dendrogram evolution
clonality
ClonEvol
dendrogram
9 months ago by
alba
• 0
3
votes
1
reply
967
views
What laptop specifications should I consider as a Bioinformatics PhD student with HPC access?
Laptop
hpc
cluster
updated 9 months ago by
Ram
45k • written 9 months ago by
Tundup
▴ 10
0
votes
1
reply
437
views
VCF Merge
VCF
MergeSTR
updated 9 months ago by
Pierre Lindenbaum
166k • written 9 months ago by
Muhammad
• 0
3
votes
4
replies
1.1k
views
Script that should show if the position of an indel is within the range of a miRNA is creating empty files. Could you help me?
miRNA
indel
8 months ago by
jhonatan.henrique
• 0
1
vote
2
replies
962
views
Issues with RAT in CAT_pack and Optimizing Relative Abundance Calculation
metagenomics
taxonomy
mag
annotation
8 weeks ago by
LuciaNhu
▴ 10
1
vote
2
replies
772
views
Hi-C interactions significance
chromatin
interactions
pvalue
Hi-C
significance
updated 7 months ago by
kalavattam
▴ 380 • written 9 months ago by
Helena
• 0
3
votes
4
replies
1.1k
views
Conceptual and statistical help in creating a synthetic RNAseq cohort from a real-world cohort of samples
statistics
DESeq2
RNAseq
updated 9 months ago by
ATpoint
89k • written 9 months ago by
K.patel5
▴ 150
0
votes
0
replies
393
views
StringTie error
DE
RNA-seq
StringTie
updated 9 months ago by
Ram
45k • written 9 months ago by
SHN
▴ 40
0
votes
0
replies
335
views
A problem with a plink file made from a VCF
plink
vcf
9 months ago by
HoWI
• 0
1
vote
2
replies
688
views
Annotating bacterial intergenic regions
bacteria
gene
intergenic
annotation
updated 9 months ago by
dthorbur
★ 3.1k • written 9 months ago by
Gio
▴ 10
0
votes
0
replies
308
views
KEGGREST to retrieve some data from KEGG
genes
keggLink
9 months ago by
mrashad
▴ 80
1
vote
1
reply
597
views
Creating adjacency matrix from collapsed row values in R
adjacency
reshape2
matrix
r
9 months ago by
ARP
▴ 10
1
vote
5
replies
1.2k
views
Deducing AIRR-seq Library Generation From SRA Data
generation
SRA
airflow
primer
airrflow
9 months ago by
A Soggy Waffle
• 0
2
votes
1
reply
605
views
BWA align in human and parasite genome, and sort them
BWA
updated 9 months ago by
GenoMax
153k • written 9 months ago by
Bender
• 0
1
vote
3
replies
798
views
Use of "grep" in RNAseq trimming
RNAseq
PolyA
updated 9 months ago by
GenoMax
153k • written 9 months ago by
Luna_1215
• 0
1
vote
1
reply
500
views
Download metabolic information from databases using the NCBI Taxonomy ID
metabolism
database
R
taxonomy
ncbi
updated 9 months ago by
GenoMax
153k • written 9 months ago by
ThaiosX195
• 0
1
vote
1
reply
534
views
No change in quality score graph even after adapter removal
rna-seq
fastqc
Trimmomatic
updated 9 months ago by
dsull
★ 7.7k • written 9 months ago by
Luna
• 0
3
votes
1
reply
665
views
Regarding ClinVar's VCF file
matrix
disease
vcf
clinvar
gene
updated 9 months ago by
Jeremy Leipzig
23k • written 9 months ago by
singhankit973
▴ 20
4
votes
10
replies
1.6k
views
Single-cell dimensionality reduction and clustering
Seurat
updated 9 months ago by
ATpoint
89k • written 9 months ago by
xingyu
▴ 10
0
votes
0
replies
364
views
How to load series matrix file into SeSAMe or minfi for processing?
sesame
geo
illumina
minfi
machine-learning
updated 9 months ago by
Ram
45k • written 9 months ago by
Junk
• 0
4
votes
14
replies
5.7k
views
7 follow
Is there anyone who downloaded Azimuth packges?
Azimuth
scRNAseq
updated 9 months ago by
ATpoint
89k • written 18 months ago by
kayah
▴ 20
3
votes
10
replies
1.8k
views
Error in conversion of ensembl to gene names
Ensembl
BioMart
updated 9 months ago by
Istvan Albert
103k • written 9 months ago by
anasjamshed
▴ 140
1
vote
1
reply
770
views
Tool:
CellLocator: An Open-Source Tool for Unlocking Deeper Insights from Live-Cell Imaging
open-source
deep-learning
denoising
single-cell
incucyte
9 months ago by
Michael
▴ 10
0
votes
5
replies
1.0k
views
Which data to choose for correlation examination
correlation
WGCNA
TPM
batch
spearman
updated 8 months ago by
Zhenyu Zhang
★ 1.3k • written 9 months ago by
lyan125
▴ 10
4
votes
12
replies
1.7k
views
Transcript coverage 3' bias. Is it really that determining?
mappings
transcriptome
RNA
updated 9 months ago by
i.sudbery
22k • written 9 months ago by
Amb@r85
▴ 10
3
votes
7
replies
1.4k
views
Quantify miRNAs from whole transcriptome library (single end, TruSeq, 100bp)
miRNA
whole-transcriptome-TruSeq
updated 9 months ago by
Ram
45k • written 13 months ago by
w.denhollander
• 0
0
votes
1
reply
685
views
comparing STARsolo UMI-based directional deduplication vs umi-tools?
single-cell
starsolo
deduplication
umi-tools
updated 9 months ago by
i.sudbery
22k • written 9 months ago by
mk
▴ 310
0
votes
0
replies
351
views
Prediction of sRNA in FASTA file
FASTA
Prediction
sRNA
9 months ago by
nashwaabdulrasheed09
• 0
0
votes
0
replies
381
views
Identification of SSR markers from RNA-seq data
MISA
SSR-markers
data
RNA-seq
9 months ago by
Kutti
• 0
121,909 results • Page
47 of 2439
Recent Votes
GSEA vs GO enrichment
Blastn and Kraken2 short reads clssification
Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
Tried building a compact sequence format with 4-bit storage
Comment: Tried building a compact sequence format with 4-bit storage
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
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• 0
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Ant
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Physalia-courses
★ 2.6k
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soledad.esteban
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Recent Replies
Answer: Trouble when installing arb
by
SilentGene
▴ 120
I've got the same error when installing from `arb-6.0.6-source.tgz` and `arb-7.0-source.tgz`. Anyone has any solution?
Comment: Hifiasm is getting killed while trying to assemble a genome
by
pranavdatar01
• 0
Yes, I did check for adaptor contamination, and did not find any. I have kept all the reads with quality score of more than 30.
Comment: Hifiasm is getting killed while trying to assemble a genome
by
Panos
★ 1.8k
No overlapping reads? Have you checked for contamination?
Comment: Tried building a compact sequence format with 4-bit storage
by
Pranava
▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data
by
alison.ludzki
• 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome
by
pranavdatar01
• 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage
by
Alex Reynolds
36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome
by
Panos
★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
Comment: Is total miRNA in EV constant? Implications for library size normalization.
by
Gordon Smyth
★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage
by
Pranava
▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage
by
Matthias Zepper
5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio)
by
GenoMax
153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions
by
GenoMax
153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest
by
piffelpaff
• 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads
by
YuZJ
• 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
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